The decision was taken after Australia's team medical staff adviced the Hayden to avoid the long plane flight to help him recover from his achilles tendon injury.
Hayden will continue rehab in Brisbane with the goal of being fit for Australia's next major cricket assignment, a four-Test series against India in India.
The Australian team, minus Hayden, injured captain Ricky Ponting and fast bowler Brett Lee who has requested time off following the breakdown of his marriage, assembled in Brisbane today at Allan Border Field for a two-day camp before heading to Darwin.
Michael Clarke will take over the captaincy reins in his first full series after deputising a number of times in Ponting's absence.
Clarke said it was a relief that the ICC had finally made a decision overnight to postpone the Champions Trophy which was to have been played in troubled Pakistan.